Guatemala's top court has overturned the genocide conviction of former dictator Efrain Rios Montt, ordering that the trial be taken back to the middle of the proceedings.

The ruling on Monday threw into disarray a process that had been hailed as historic for delivering the first guilty verdict for genocide against a former Latin American leader.

Constitutional Court secretary Martin Guzman said the trial needed to go back to where it stood on April 19 to solve several appeal issues.

The ruling came 10 days after a three-judge panel convicted the 86-year-old Rios Montt of genocide and crimes against humanity for his role in massacres of Mayans during Guatemala's 36-year civil war. He was handed an 80-year prison term.

The panel found that Rios Montt knew about the slaughter of at least 1,771 Ixil Mayans in the western highlands and didn't stop it. More than 100 witnesses and experts testified about mass rapes and killings of women and children and other atrocities perpetrated by government troops. Rios Montt ruled Guatemala in 1982-83 following a coup.

Rios Montt is the first former Latin American leader convicted of such crimes in his home country and the first official acknowledgment that genocide occurred in the war - something the current president, retired General Otto Perez Molina, has denied.

Rios Montt's lawyers immediately filed an appeal, and he spent three days in prison before he was moved to a military hospital, where he remains.

The top court on Monday said it threw out his conviction because the trial should have been stopped while appeals filed by the defence were resolved.

Defence lawyer Francisco Garcia Gudiel said in an interview that he would seek the former dictator's freedom.

This article appeared in the South China Morning Post print edition as Court orders dictator to restand late part of trial